OpenRaiser/Intern-Atlas huggingface dataset:
Generative Models for Automatic Chemical Design
Venue: arXiv cs.LG 2019
Year: 2019

Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to optimize properties from molecular structures. On the other hand, inverse approaches map properties to structures, thus expediting the design of novel useful compounds. In this chapter, we examine the way in which current deep generative models are addressing the inverse chemical discovery paradigm. We begin by revisiting early inverse design algorithms. Then, we introduce generative models for molecular systems and categorize them according to their architecture and molecular representation. Using this classification, we review the evolution and performance of important molecular generation schemes reported in the literature. Finally, we conclude highlighting the prospects and challenges of generative models as cutting edge tools in materials discovery.
A Neural Attention Model for Adaptive Learning of Social Friends' Preferences
Venue: arXiv cs.IR 2019
Year: 2019

Social-based recommendation systems exploit the selections of friends to combat the data sparsity on user preferences, and improve the recommendation accuracy of the collaborative filtering strategy. The main challenge is to capture and weigh friends' preferences, as in practice they do necessarily match. In this paper, we propose a Neural Attention mechanism for Social collaborative filtering, namely NAS. We design a neural architecture, to carefully compute the non-linearity in friends' preferences by taking into account the social latent effects of friends on user behavior. In addition, we introduce a social behavioral attention mechanism to adaptively weigh the influence of friends on user preferences and consequently generate accurate recommendations. Our experiments on publicly available datasets demonstrate the effectiveness of the proposed NAS model over other state-of-the-art methods. Furthermore, we study the effect of the proposed social behavioral attention mechanism and show that it is a key factor to our model's performance.
Data mining Mandarin tone contour shapes
Venue: arXiv cs.CL 2019
Year: 2019

In spontaneous speech, Mandarin tones that belong to the same tone category may exhibit many different contour shapes. We explore the use of data mining and NLP techniques for understanding the variability of tones in a large corpus of Mandarin newscast speech. First, we adapt a graph-based approach to characterize the clusters (fuzzy types) of tone contour shapes observed in each tone n-gram category. Second, we show correlations between these realized contour shape types and a bag of automatically extracted linguistic features. We discuss the implications of the current study within the context of phonological and information theory.
Machine Learning based Prediction of Hierarchical Classification of Transposable Elements
Venue: arXiv cs.LG 2019
Year: 2019

Transposable Elements (TEs) or jumping genes are the DNA sequences that have an intrinsic capability to move within a host genome from one genomic location to another. Studies show that the presence of a TE within or adjacent to a functional gene may alter its expression. TEs can also cause an increase in the rate of mutation and can even mediate duplications and large insertions and deletions in the genome, promoting gross genetic rearrangements. Thus, the proper classification of the identified jumping genes is essential to understand their genetic and evolutionary effects in the genome. While computational methods have been developed that perform either binary classification or multi-label classification of TEs, few studies have focused on their hierarchical classification. The state-of-the-art machine learning classification method utilizes a Multi-Layer Perceptron (MLP), a class of neural network, for hierarchical classification of TEs. However, the existing methods have limited accuracy in classifying TEs. A more effective classifier, which can explain the role of TEs in germline and somatic evolution, is needed. In this study, we examine the performance of a variety of machine learning (ML) methods. And eventually, propose a robust approach for the hierarchical classification of TEs, with higher accuracy, using Support Vector Machines (SVM).
Towards a formally verified implementation of the MimbleWimble cryptocurrency protocol
Venue: arXiv cs.CR 2019
Year: 2019

MimbleWimble is a privacy-oriented cryptocurrency technology encompassing security and scalability properties that distinguish it from other protocols of the kind. In this paper we present and briefly discuss those properties and outline the basis of a model-driven verification approach to address the certification of the correctness of a particular implementation of the protocol.
Shortest Reconfiguration of Perfect Matchings via Alternating Cycles
Venue: arXiv cs.DS 2019
Year: 2019

Motivated by adjacency in perfect matching polytopes, we study the shortest reconfiguration problem of perfect matchings via alternating cycles. Namely, we want to find a shortest sequence of perfect matchings which transforms one given perfect matching to another given perfect matching such that the symmetric difference of each pair of consecutive perfect matchings is a single cycle. The problem is equivalent to the combinatorial shortest path problem in perfect matching polytopes. We prove that the problem is NP-hard even when a given graph is planar or bipartite, but it can be solved in polynomial time when the graph is outerplanar.
A Deep Image Compression Framework for Face Recognition
Venue: arXiv cs.CV 2019
Year: 2019

Face recognition technology has advanced rapidly and has been widely used in various applications. Due to the extremely huge amount of data of face images and the large computing resources required correspondingly in large-scale face recognition tasks, there is a requirement for a face image compression approach that is highly suitable for face recognition tasks. In this paper, we propose a deep convolutional autoencoder compression network for face recognition tasks. In the compression process, deep features are extracted from the original image by the convolutional neural networks to produce a compact representation of the original image, which is then encoded and saved by existing codec such as PNG. This compact representation is utilized by the reconstruction network to generate a reconstructed image of the original one. In order to improve the face recognition accuracy when the compression framework is used in a face recognition system, we combine this compression framework with a existing face recognition network for joint optimization. We test the proposed scheme and find that after joint training, the Labeled Faces in the Wild (LFW) dataset compressed by our compression framework has higher face verification accuracy than that compressed by JPEG2000, and is much higher than that compressed by JPEG.
Tracking system of Mine Patrol Robot for Low Illumination Environment
Venue: arXiv cs.CV 2019
Year: 2019

Computer vision has received a significant attention in recent years, which is one of the important parts for robots to apperceive external environment. Discriminative Correlation Filter (DCF) based trackers gained more popularity due to their efficiency, however, tracking in low-illumination environments is a challenging problem, not yet successfully addressed in the literature. In this work, we tackle the problems by introducing Low-Illumination Long-term Correlation Tracker (LLCT). First, fused features only including HOG and Color Names are employed to boost the tracking efficiency. Second, we used the standard PCA to reduction scheme in the translation and scale estimation phase for accelerating. Third, we learned a long-term correlation filter to keep the long-term memory ability. Finally, update memory templates with interval updates, then re-match existing and initial templates every few frames to maintain template accuracy. The extensive experiments on popular Object Tracking Benchmark OTB-50 datasets have demonstrated that the proposed tracker outperforms the state-of-the-art trackers significantly achieves a high real-time (33FPS) performance. In addition, the proposed approach can be integrated easily in robot system and the running speed performed well. The experimental results show that the novel tracker performance in low-illumination environment is better than that of general trackers.
A Case Study of Deep-Learned Activations via Hand-Crafted Audio Features
Venue: arXiv cs.SD 2019
Year: 2019

The explainability of Convolutional Neural Networks (CNNs) is a particularly challenging task in all areas of application, and it is notably under-researched in music and audio domain. In this paper, we approach explainability by exploiting the knowledge we have on hand-crafted audio features. Our study focuses on a well-defined MIR task, the recognition of musical instruments from user-generated music recordings. We compute the similarity between a set of traditional audio features and representations learned by CNNs. We also propose a technique for measuring the similarity between activation maps and audio features which typically presented in the form of a matrix, such as chromagrams or spectrograms. We observe that some neurons' activations correspond to well-known classical audio features. In particular, for shallow layers, we found similarities between activations and harmonic and percussive components of the spectrum. For deeper layers, we compare chromagrams with high-level activation maps as well as loudness and onset rate with deep-learned embeddings.
Super-Resolution of PROBA-V Images Using Convolutional Neural Networks
Venue: arXiv cs.CV 2019
Year: 2019

ESA's PROBA-V Earth observation satellite enables us to monitor our planet at a large scale, studying the interaction between vegetation and climate and provides guidance for important decisions on our common global future. However, the interval at which high resolution images are recorded spans over several days, in contrast to the availability of lower resolution images which is often daily. We collect an extensive dataset of both, high and low resolution images taken by PROBA-V instruments during monthly periods to investigate Multi Image Super-resolution, a technique to merge several low resolution images to one image of higher quality. We propose a convolutional neural network that is able to cope with changes in illumination, cloud coverage and landscape features which are challenges introduced by the fact that the different images are taken over successive satellite passages over the same region. Given a bicubic upscaling of low resolution images taken under optimal conditions, we find the Peak Signal to Noise Ratio of the reconstructed image of the network to be higher for a large majority of different scenes. This shows that applied machine learning has the potential to enhance large amounts of previously collected earth observation data during multiple satellite passes.
Deformable Tube Network for Action Detection in Videos
Venue: arXiv cs.CV 2019
Year: 2019

We address the problem of spatio-temporal action detection in videos. Existing methods commonly either ignore temporal context in action recognition and localization, or lack the modelling of flexible shapes of action tubes. In this paper, we propose a two-stage action detector called Deformable Tube Network (DTN), which is composed of a Deformation Tube Proposal Network (DTPN) and a Deformable Tube Recognition Network (DTRN) similar to the Faster R-CNN architecture. In DTPN, a fast proposal linking algorithm (FTL) is introduced to connect region proposals across frames to generate multiple deformable action tube proposals. To perform action detection, we design a 3D convolution network with skip connections for tube classification and regression. Modelling action proposals as deformable tubes explicitly considers the shape of action tubes compared to 3D cuboids. Moreover, 3D convolution based recognition network can learn temporal dynamics sufficiently for action detection. Our experimental results show that we significantly outperform the methods with 3D cuboids and obtain the state-of-the-art results on both UCF-Sports and AVA datasets.
Probabilistic Multilayer Regularization Network for Unsupervised 3D Brain Image Registration
Venue: arXiv cs.CV 2019
Year: 2019

Brain image registration transforms a pair of images into one system with the matched imaging contents, which is of essential importance for brain image analysis. This paper presents a novel framework for unsupervised 3D brain image registration by capturing the feature-level transformation relationships between the unaligned image and reference image. To achieve this, we develop a feature-level probabilistic model to provide the direct regularization to the hidden layers of two deep convolutional neural networks, which are constructed from two input images. This model design is developed into multiple layers of these two networks to capture the transformation relationships at different levels. We employ two common benchmark datasets for 3D brain image registration and perform various experiments to evaluate our method. Experimental results show that our method clearly outperforms state-of-the-art methods on both benchmark datasets by a large margin.
A Need for Trust in Conversational Interface Research
Venue: arXiv cs.HC 2019
Year: 2019

Across several branches of conversational interaction research including interactions with social robots, embodied agents, and conversational assistants, users have identified trust as a critical part of those interactions. Nevertheless, there is little agreement on what trust means within these sort of interactions or how trust can be measured. In this paper, we explore some of the dimensions of trust as it has been understood in previous work and we outline some of the ways trust has been measured in the hopes of furthering discussion of the concept across the field.
Towards Automated Application-Specific Software Stacks
Venue: arXiv cs.CR 2019
Year: 2019

Software complexity has increased over the years. One common way to tackle this complexity during development is to encapsulate features into a shared library. This allows developers to reuse already implemented features instead of reimplementing them over and over again. However, not all features provided by a shared library are actually used by an application. As a result, an application using shared libraries loads unused code into memory, which an attacker can use to perform code-reuse and similar types of attacks. The same holds for applications written in a scripting language such as PHP or Ruby: The interpreter typically offers much more functionality than is actually required by the application and hence provides a larger overall attack surface. In this paper, we tackle this problem and propose a first step towards automated application-specific software stacks. We present a compiler extension capable of removing unneeded code from shared libraries and---with the help of domain knowledge---also capable of removing unused functionalities from an interpreter's code base during the compilation process. Our evaluation against a diverse set of real-world applications, among others Nginx, Lighttpd, and the PHP interpreter, removes on average 71.3% of the code in musl-libc, a popular libc implementation. The evaluation on web applications show that a tailored PHP interpreter can mitigate entire vulnerability classes, as is the case for OpenConf. We demonstrate the applicability of our debloating approach by creating an application-specific software stack for a Wordpress web application: we tailor the libc library to the Nginx web server and PHP interpreter, whereas the PHP interpreter is tailored to the Wordpress web application. In this real-world scenario, the code of the libc is decreased by 65.1% in total, thereby reducing the available code for code-reuse attacks.
Comparison of research productivity of Italian and Norwegian professors and universities
Venue: arXiv cs.DL 2019
Year: 2019

This is the first ever attempt of application in a country other than Italy of a research efficiency indicator (FSS), to assess and compare the performance of professors and universities, within and between countries. A special attention has been devoted to the presentation of the methodology developed to set up a common field classification scheme of professors, and to overcome the limited availability of comparable input data. Results of the comparison between countries, carried out in the 2011-2015 period, show similar average performances of professors, but noticeable differences in the distributions, whereby Norwegian professors are more concentrated in the tails. Norway shows notable higher performance in Mathematics and Earth and Space Sciences, while Italy in Biomedical Research and Engineering.
Novel evaluation of surgical activity recognition models using task-based efficiency metrics
Venue: arXiv cs.CV 2019
Year: 2019

Purpose: Surgical task-based metrics (rather than entire procedure metrics) can be used to improve surgeon training and, ultimately, patient care through focused training interventions. Machine learning models to automatically recognize individual tasks or activities are needed to overcome the otherwise manual effort of video review. Traditionally, these models have been evaluated using frame-level accuracy. Here, we propose evaluating surgical activity recognition models by their effect on task-based efficiency metrics. In this way, we can determine when models have achieved adequate performance for providing surgeon feedback via metrics from individual tasks. Methods: We propose a new CNN-LSTM model, RP-Net-V2, to recognize the 12 steps of robotic-assisted radical prostatectomies (RARP). We evaluated our model both in terms of conventional methods (e.g. Jaccard Index, task boundary accuracy) as well as novel ways, such as the accuracy of efficiency metrics computed from instrument movements and system events. Results: Our proposed model achieves a Jaccard Index of 0.85 thereby outperforming previous models on robotic-assisted radical prostatectomies. Additionally, we show that metrics computed from tasks automatically identified using RP-Net-V2 correlate well with metrics from tasks labeled by clinical experts. Conclusions: We demonstrate that metrics-based evaluation of surgical activity recognition models is a viable approach to determine when models can be used to quantify surgical efficiencies. We believe this approach and our results illustrate the potential for fully automated, post-operative efficiency reports.
The Indirect Convolution Algorithm
Venue: arXiv cs.CV 2019
Year: 2019

Deep learning frameworks commonly implement convolution operators with GEMM-based algorithms. In these algorithms, convolution is implemented on top of matrix-matrix multiplication (GEMM) functions, provided by highly optimized BLAS libraries. Convolutions with 1x1 kernels can be directly represented as a GEMM call, but convolutions with larger kernels require a special memory layout transformation - im2col or im2row - to fit into GEMM interface. The Indirect Convolution algorithm provides the efficiency of the GEMM primitive without the overhead of im2col transformation. In contrast to GEMM-based algorithms, the Indirect Convolution does not reshuffle the data to fit into the GEMM primitive but introduces an indirection buffer - a buffer of pointers to the start of each row of image pixels. This broadens the application of our modified GEMM function to convolutions with arbitrary kernel size, padding, stride, and dilation. The Indirect Convolution algorithm reduces memory overhead proportionally to the number of input channels and outperforms the GEMM-based algorithm by up to 62% on convolution parameters which involve im2col transformations in GEMM-based algorithms. This, however, comes at cost of minor performance reduction on 1x1 stride-1 convolutions.
Linear Size Sparsifier and the Geometry of the Operator Norm Ball
Venue: arXiv cs.DS 2019
Year: 2019

The Matrix Spencer Conjecture asks whether given $n$ symmetric matrices in $\mathbb{R}^{n \times n}$ with eigenvalues in $[-1,1]$ one can always find signs so that their signed sum has singular values bounded by $O(\sqrt{n})$. The standard approach in discrepancy requires proving that the convex body of all good fractional signings is large enough. However, this question has remained wide open due to the lack of tools to certify measure lower bounds for rather small non-polyhedral convex sets. A seminal result by Batson, Spielman and Srivastava from 2008 shows that any undirected graph admits a linear size spectral sparsifier. Again, one can define a convex body of all good fractional signings. We can indeed prove that this body is close to most of the Gaussian measure. This implies that a discrepancy algorithm by the second author can be used to sample a linear size sparsifer. In contrast to previous methods, we require only a logarithmic number of sampling phases.
Seeing Under the Cover: A Physics Guided Learning Approach for In-Bed Pose Estimation
Venue: arXiv cs.CV 2019
Year: 2019

Human in-bed pose estimation has huge practical values in medical and healthcare applications yet still mainly relies on expensive pressure mapping (PM) solutions. In this paper, we introduce our novel physics inspired vision-based approach that addresses the challenging issues associated with the in-bed pose estimation problem including monitoring a fully covered person in complete darkness. We reformulated this problem using our proposed Under the Cover Imaging via Thermal Diffusion (UCITD) method to capture the high resolution pose information of the body even when it is fully covered by using a long wavelength IR technique. We proposed a physical hyperparameter concept through which we achieved high quality groundtruth pose labels in different modalities. A fully annotated in-bed pose dataset called Simultaneously-collected multimodal Lying Pose (SLP) is also formed/released with the same order of magnitude as most existing large-scale human pose datasets to support complex models' training and evaluation. A network trained from scratch on it and tested on two diverse settings, one in a living room and the other in a hospital room showed pose estimation performance of 99.5% and 95.7% in PCK0.2 standard, respectively. Moreover, in a multi-factor comparison with a state-of-the art in-bed pose monitoring solution based on PM, our solution showed significant superiority in all practical aspects by being 60 times cheaper, 300 times smaller, while having higher pose recognition granularity and accuracy.
Sketched MinDist
Venue: arXiv cs.CG 2019
Year: 2019

We consider sketch vectors of geometric objects $J$ through the \mindist function \[ v_i(J) = \inf_{p \in J} \|p-q_i\| \] for $q_i \in Q$ from a point set $Q$. Collecting the vector of these sketch values induces a simple, effective, and powerful distance: the Euclidean distance between these sketched vectors. This paper shows how large this set $Q$ needs to be under a variety of shapes and scenarios. For hyperplanes we provide direct connection to the sensitivity sample framework, so relative error can be preserved in $d$ dimensions using $Q = O(d/\varepsilon^2)$. However, for other shapes, we show we need to enforce a minimum distance parameter $ρ$, and a domain size $L$. For $d=2$ the sample size $Q$ then can be $\tilde{O}((L/ρ) \cdot 1/\varepsilon^2)$. For objects (e.g., trajectories) with at most $k$ pieces this can provide stronger \emph{for all} approximations with $\tilde{O}((L/ρ)\cdot k^3 / \varepsilon^2)$ points. Moreover, with similar size bounds and restrictions, such trajectories can be reconstructed exactly using only these sketch vectors.